package analysis;


/**
 * @author Mathieu Rousseau
 * @email mathieu.rousseau3@mail.mcgill.ca
 */


/** ------------------------------------------------------------------------------------------------------------------
 * start of BurnInAnalyzerMain class
 * ------------------------------------------------------------------------------------------------------------------  **/
public class BurnInAnalyzerMain {

	/*  start of main method  */
	public static void main(String[] args) {
		
		//  parameters for the BurnInAnalyzer program
		String experimentNameOne, experimentNameTwo;
		int numberOfStructures, windowSize;
		
		
		//  BurnInAnalyzer program object
		BurnInAnalyzer burnInAnalyzer = new BurnInAnalyzer();
		
		
		
		
		
		
		/** ------------------------------------------------------------------------------------------------------------------
		 * 
		 * 
		 * 								HARDCODING OF PARAMETERS
		 * 
		 * 
		 * ------------------------------------------------------------------------------------------------------------------  */
		
		
		
		
		//  specify the names of the experiments
		//  this is the common suffix to all structure filenames from each of the runs (i.e. filenames = structure_####_experimentName.pdb)
		experimentNameOne = "HB119[1]";
		experimentNameTwo = "HB119[4]";
		
		
		//  specify the number of structures from each experiment 
		numberOfStructures = 200;
		
		
		//  specify the size of the sliding window
		windowSize = 10;
		
		
		
		
		/** ------------------------------------------------------------------------------------------------------------------
		 * 
		 * 
		 * 								END OF HARDCODING OF PARAMETERS
		 * 
		 * 
		 * ------------------------------------------------------------------------------------------------------------------  */
		
		
		
		
		
		//  add all of the parameters to the arguments array
		args = new String[4];
		args[0] = experimentNameOne;
		args[1] = experimentNameTwo;
		args[2] = String.valueOf(numberOfStructures);
		args[3] = String.valueOf(windowSize);
		
		
		//  run the BurnInAnalyzer program
		burnInAnalyzer.run(args);
		
		
	}/*  end of main method  */

}/*  end of BurnInAnalyzerMain class  */
